[Re] Model of thalamocortical slow-wave sleep oscillations and transitions to activated states

[Mathilde-Reynes]

Original article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6757797/

PDF URL: https://github.com/Mathilde-Reynes/ReynesAussel2024/blob/a732939b013c7966631ef9e742c98d29ba311934/Submission/%5BRe%5DReynesAussel2024.pdf
Metadata URL: https://github.com/Mathilde-Reynes/ReynesAussel2024/blob/a732939b013c7966631ef9e742c98d29ba311934/Submission/metadata.yaml
Code URL: https://github.com/Mathilde-Reynes/ReynesAussel2024/tree/a732939b013c7966631ef9e742c98d29ba311934/Model

Scientific domain: Computational Neuroscience
Programming language: Python (brian2)
Suggested editor: Benoît Girard
Suggested reviewers: Qihong Lu; Ozan Caglayan; Pierre Enel

[rougier]

Very sorry for the long delay, we'll assign an editor soon.

[rougier]

@benoit-girard Can you edit this submission, I think it's a perfect fit for you.

[rougier]

I'll handle the submission.
Disclaimer: I'm in the same lab as authors.

[rougier]

@benoit-girard @apdavison @heplesser @vitay @mstimberg @pietromarchesi @stephanmg

Can your review this submission on "Model of thalamocortical slow-wave sleep oscillations and transitions to activated states"

[apdavison]

yes, I can review this.

[heplesser]

I can review as well.

[mstimberg]

I'd be happy to review this, too (but certainly do not mind leaving it to the two who agreed to review earlier, either) 😊

[rougier]

Thank you very much.@apdavison @heplesser @mstimberg.

@apdavison @heplesser (since you were first to answer) you can start the review (and if you can do it before Christmas that would be great) and feel free to ask questions if needed.
@mstimberg Thanks again, I think I've other submission waiting for reviewers.

[rougier]

@apdavison @heplesser Any chance to get your reviews by next Monday (before Christmas)?

[apdavison]

@rougier I'm afraid I don't think it will be possible before Christmas. I've pencilled this in for the first full week in January, I'm targeting January 10th.

[stephanmg]

@benoit-girard @apdavison @heplesser @vitay @mstimberg @pietromarchesi @stephanmg

Can your review this submission on "Model of thalamocortical slow-wave sleep oscillations and transitions to activated states"

terribly sorry, somehow this went under the radar for me, if help is still needed, happy to assist!

[heplesser]

I am also aiming for the first week of 2025.

…

________________________________ From: Stephan Grein ***@***.***> Sent: Thursday, December 19, 2024 6:20:17 PM To: ReScience/submissions ***@***.***> Cc: Hans Ekkehard Plesser ***@***.***>; Mention ***@***.***> Subject: Re: [ReScience/submissions] [Re] Model of thalamocortical slow-wave sleep oscillations and transitions to activated states (Issue #87) @benoit-girard<https://github.com/benoit-girard> @apdavison<https://github.com/apdavison> @heplesser<https://github.com/heplesser> @vitay<https://github.com/vitay> @mstimberg<https://github.com/mstimberg> @pietromarchesi<https://github.com/pietromarchesi> @stephanmg<https://github.com/stephanmg> Can your review this submission on "Model of thalamocortical slow-wave sleep oscillations and transitions to activated states" terribly sorry, somehow this went under the radar for me, if help is still needed, happy to assist! — Reply to this email directly, view it on GitHub<#87 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAICWPD4L3JYVORMQIYGJG32GL55DAVCNFSM6AAAAABNGQ7AI6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNJVGIZDENZWGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[apdavison]

I have started reviewing the submission, and I will post more complete comments soon; however, I would like here to make a preliminary suggestion which will both (i) help me finish the review and (ii) make the re-implemented model more reproducible.

I was able to run python Thalamo_cortical.py, which completes without error. The problem is that to reproduce the data for the figures, I need to uncomment certain lines in Thalamo_cortical.py and, for some figures, also in other files. It takes a lot of reading and checking code to make sure the correct lines have been uncommented and re-commented.

If the authors have time, it would be very helpful to put the commented-out lines into a dictionary, or into functions, so that all the changes are controlled by a single parameter (ideally provided on the command-line, e.g., python Thalamo_cortical.py Figure4). Similarly, saving the raw data should be controlled by another parameter.